ClinVar Genomic variation as it relates to human health
NM_000053.4(ATP7B):c.1908dup (p.Asn637fs)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_000053.4(ATP7B):c.1908dup (p.Asn637fs)
Variation ID: 2679800 Accession: VCV002679800.2
- Type and length
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Duplication, 1 bp
- Location
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Cytogenetic: 13q14.3 13: 51961874-51961875 (GRCh38) [ NCBI UCSC ] 13: 52536010-52536011 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Dec 30, 2023 Feb 14, 2024 Sep 22, 2023 - HGVS
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Nucleotide Protein Molecular
consequenceNM_000053.4:c.1908dup MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_000044.2:p.Asn637fs frameshift NM_001005918.3:c.1869+2997dup intron variant NM_001243182.2:c.1575dup NP_001230111.1:p.Asn526fs frameshift NM_001330578.2:c.1908dup NP_001317507.1:p.Asn637fs frameshift NM_001330579.2:c.1869+2997dup intron variant NM_001406511.1:c.1908dup NP_001393440.1:p.Asn637fs frameshift NM_001406512.1:c.1908dup NP_001393441.1:p.Asn637fs frameshift NM_001406513.1:c.1908dup NP_001393442.1:p.Asn637fs frameshift NM_001406514.1:c.1875dup NP_001393443.1:p.Asn626fs frameshift NM_001406515.1:c.1908dup NP_001393444.1:p.Asn637fs frameshift NM_001406516.1:c.1908dup NP_001393445.1:p.Asn637fs frameshift NM_001406517.1:c.1812dup NP_001393446.1:p.Asn605fs frameshift NM_001406518.1:c.1812dup NP_001393447.1:p.Asn605fs frameshift NM_001406519.1:c.1908dup NP_001393448.1:p.Asn637fs frameshift NM_001406520.1:c.1908dup NP_001393449.1:p.Asn637fs frameshift NM_001406521.1:c.1908dup NP_001393450.1:p.Asn637fs frameshift NM_001406522.1:c.1908dup NP_001393451.1:p.Asn637fs frameshift NM_001406523.1:c.1908dup NP_001393452.1:p.Asn637fs frameshift NM_001406524.1:c.1875dup NP_001393453.1:p.Asn626fs frameshift NM_001406525.1:c.1908dup NP_001393454.1:p.Asn637fs frameshift NM_001406526.1:c.1908dup NP_001393455.1:p.Asn637fs frameshift NM_001406527.1:c.1908dup NP_001393456.1:p.Asn637fs frameshift NM_001406528.1:c.1908dup NP_001393457.1:p.Asn637fs frameshift NM_001406530.1:c.1812dup NP_001393459.1:p.Asn605fs frameshift NM_001406531.1:c.1869+2997dup intron variant NM_001406532.1:c.1869+2997dup intron variant NM_001406534.1:c.1908dup NP_001393463.1:p.Asn637fs frameshift NM_001406535.1:c.1908dup NP_001393464.1:p.Asn637fs frameshift NM_001406536.1:c.1812dup NP_001393465.1:p.Asn605fs frameshift NM_001406537.1:c.1908dup NP_001393466.1:p.Asn637fs frameshift NM_001406538.1:c.1908dup NP_001393467.1:p.Asn637fs frameshift NM_001406539.1:c.1479dup NP_001393468.1:p.Asn494fs frameshift NM_001406540.1:c.1869+2997dup intron variant NM_001406541.1:c.1869+2997dup intron variant NM_001406542.1:c.1869+2997dup intron variant NM_001406543.1:c.1773+2997dup intron variant NM_001406544.1:c.1773+2997dup intron variant NM_001406545.1:c.1708-4268dup intron variant NM_001406546.1:c.1869+2997dup intron variant NM_001406547.1:c.1708-4268dup intron variant NM_001406548.1:c.1286-11714dup intron variant NC_000013.11:g.51961878dup NC_000013.10:g.52536014dup NG_008806.1:g.54620dup - Protein change
- N494fs, N526fs, N605fs, N626fs, N637fs
- Other names
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- Canonical SPDI
- NC_000013.11:51961874:GGGG:GGGGG
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
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The frequency of the allele represented by this VCV record.
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- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
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Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
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The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
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The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
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The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
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The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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ATP7B | - | - |
GRCh38 GRCh37 |
2901 | 3044 |
Conditions - Germline
Condition
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The condition for this variant-condition (RCV) record in ClinVar. |
Classification
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The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
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The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
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The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
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The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Pathogenic/Likely pathogenic (2) |
criteria provided, multiple submitters, no conflicts
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Sep 22, 2023 | RCV003464938.3 |
Submissions - Germline
Classification
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The submitted germline classification for each SCV record. (Last evaluated) |
Review status
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Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
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The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
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The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
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This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Likely pathogenic
(Jun 24, 2023)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
Affected status: unknown
Allele origin:
unknown
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Baylor Genetics
Accession: SCV004216393.1
First in ClinVar: Dec 30, 2023 Last updated: Dec 30, 2023 |
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Pathogenic
(Sep 22, 2023)
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criteria provided, single submitter
Method: clinical testing
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Wilson disease
Affected status: unknown
Allele origin:
germline
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Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV004325309.1
First in ClinVar: Feb 14, 2024 Last updated: Feb 14, 2024 |
Comment:
This sequence change creates a premature translational stop signal (p.Asn637Glnfs*118) in the ATP7B gene. It is expected to result in an absent or disrupted protein … (more)
This sequence change creates a premature translational stop signal (p.Asn637Glnfs*118) in the ATP7B gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ATP7B are known to be pathogenic (PMID: 10441329, 16283883). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with ATP7B-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. (less)
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Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Frameshift and nonsense mutations in the gene for ATPase7B are associated with severe impairment of copper metabolism and with an early clinical manifestation of Wilson's disease. | Gromadzka G | Clinical genetics | 2005 | PMID: 16283883 |
Null mutation of the murine ATP7B (Wilson disease) gene results in intracellular copper accumulation and late-onset hepatic nodular transformation. | Buiakova OI | Human molecular genetics | 1999 | PMID: 10441329 |
Text-mined citations for this variant ...
HelpRecord last updated Sep 30, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.